Waterborne coatings have obtained more and more attention from researchers with increasing concerns in environmental protection, and have the advantages of being green, environmentally friendly and safe. However, the introduction of hydrophilic groups leads to lower hydrophobicity and it is difficult to meet the requirements of complex application environments. Herein, we proposed an optimization approach of waterborne polyurethane (WPU) with vinyl tris(β-methoxyethoxy) silane (A172), and it was found that the surface roughness, mechanical properties, thermal stability and water resistance of WPU will be increased to a certain extent with the addition of A172. Moreover, the hydrophobicity of the coating film is best when the silicon content is 10% of the acrylic monomer mass and the water contact angle reaches 100°, which could exceed two-thirds of the research results in the last decade. Therefore, our study can provide some theoretical basis for the research of hydrophobic polyurethane coatings.